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Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes. [ABSTRACT FROM AUTHOR]

Recently, the large migratory fishes of the family Serrasalmidae (Piaractus brachypomus and P. orinoquensis) were described as restricted to the Orinoco and Amazon basins. Both species provide important ecosystem services. They also are an important fisheries resource, which has caused that their populations have decreased in recent years. National fisheries policies still consider both species as one, which leads to inefficiencies in their management and conservation. The aim of this study was to genetically characterize these two species, using microsatellite and mitochondrial markers, and discuss the implication of these results for conservation and management. We found that both species have moderate genetic diversity and varied patterns of genetic distribution in the fluvial landscape. Piaractus brachypomus presented genetic diversity of A=6.5; He=0.72; Ho=0.67; Ĥ=1.000; 1=0.0092, three management units related to the evolutionary process of the Amazon basin and the effective sizes of local populations were smaller compared to P. orinoquensis, which presented genetic diversity of A=6.1; He=0.66; Ho=0.55; Ĥ=0.968; 1=0.010 and comprises only one management unit. These results demonstrate the need to design management policies that focus on species and geographically restricted populations. [ABSTRACT FROM AUTHOR]

The large catfish Pseudoplatystoma punctifer plays an important role as a top predator in the Amazonian Basin ecosystem. The Madeira River is the largest tributary of the Amazon River marked by a series of rapids and waterfalls. Between 2011 and 2012 some of the rapids were submerged by two hydroelectric dams. Upstream and downstream of the rapids are two sub-basins Mamoré/Guaporé and lower Madeira, respectively. Using mitochondrial and microsatellite markers, we estimated genetic diversity, genetic differentiation, and gene flow between sub-basins and tested if the rapids functioned as barriers limiting the gene flow for this species of catfish. We identified three population clusters, one representing the individuals from the Mamoré/Guaporé sub-basin (upstream) and the other two representing the individuals from the lower Madeira sub-basin (downstream). The rapids restricted but did not block gene flow, which corroborates a clinal pattern of genetic differentiation. [ABSTRACT FROM AUTHOR]

Nesting site selection is of great ecological and evolutionary importance for turtles, because it is a key determinant of individual reproductive success. In this study we evaluated the effects of two types of nesting substrate (sand bank and clay banks) on the incubation success of a generalist nesting species, Podocnemis unifilis, in a floodplain area in the Brazilian Amazon. Nesting characteristics were recorded during the nesting seasons of 2012-2014, when 634 nests were monitored throughout the incubation period. Mean size of laying females did not vary between substrate types (sand = 24.71 cm; clay = 25.44 cm; P = 0.2054), nor was clutch size related to females' sizes. However, females that nested on sand bank exhibited a clearer pattern of nest positioning relative to distances to vegetation and water line than those laying eggs on clay banks. Mean egg size (40.24 ± 2.68 mm) and weight (21.09 ± 5.46 g) did not vary between types of nesting substrate, and there was no variation in clutch size across the reproductive seasons for either substrate. On the other hand, clutch sizes were higher in nests in clay banks (28 ± 8) than those that were deposited in sand bank (22 ± 7). Mean incubation time was shorter in sand bank (62 ± 5.98) than in clay banks (77 ± 4.33). Although eclosion success for sand and clay nests was high (84.82 and 72.97%, respectively), incubation success was relatively low in both substrate types (sand = 57.34%; clay = 25.80%). On sand bank, clutch losses were mainly due to human predation (16%), on clay banks, human predation also affected 16% of the nests, but floods compromised another 30%. Natural predation was mostly due to ovivory by the lizard Tupinambis teguixin, although fire ants, Solenopsis geminata, also contributed to egg predation on clay banks. Hatchlings incubated on sand bank were on average larger and heavier than those from clay banks nests. Our results suggest that differences found in the life histories of different populations of P. unifilis reflect flexible responses that are largely linked to the diversity of habitats this species utilizes for nesting. Furthermore, the presence of source-sink and habitat patches should be considered for short term population management, beyond the creation of networks of reserves that incorporate and protect a variety of nesting sites that these small local groups depend on for their survival. [ABSTRACT FROM AUTHOR]

Nesting site selection is of great ecological and evolutionary importance for turtles, because it is a key determinant of individual reproductive success. In this study we evaluated the effects of two types of nesting substrate (sand bank and clay banks) on the incubation success of a generalist nesting species, Podocnemis unifilis, in a floodplain area in the Brazilian Amazon. Nesting characteristics were recorded during the nesting seasons of 2012-2014, when 634 nests were monitored throughout the incubation period. Mean size of laying females did not vary between substrate types (sand = 24.71 cm; clay = 25.44 cm; P = 0.2054), nor was clutch size related to females' sizes. However, females that nested on sand bank exhibited a clearer pattern of nest positioning relative to distances to vegetation and water line than those laying eggs on clay banks. Mean egg size (40.24 ± 2.68 mm) and weight (21.09 ± 5.46 g) did not vary between types of nesting substrate, and there was no variation in clutch size across the reproductive seasons for either substrate. On the other hand, clutch sizes were higher in nests in clay banks (28 ± 8) than those that were deposited in sand bank (22 ± 7). Mean incubation time was shorter in sand bank (62 ± 5.98) than in clay banks (77 ± 4.33). Although eclosion success for sand and clay nests was high (84.82 and 72.97%, respectively), incubation success was relatively low in both substrate types (sand = 57.34%; clay = 25.80%). On sand bank, clutch losses were mainly due to human predation (16%), on clay banks, human predation also affected 16% of the nests, but floods compromised another 30%. Natural predation was mostly due to ovivory by the lizard Tupinambis teguixin, although fire ants, Solenopsis geminata, also contributed to egg predation on clay banks. Hatchlings incubated on sand bank were on average larger and heavier than those from clay banks nests. Our results suggest that differences found in the life histories of different populations of P. unifilis reflect flexible responses that are largely linked to the diversity of habitats this species utilizes for nesting. Furthermore, the presence of source-sink and habitat patches should be considered for short term population management, beyond the creation of networks of reserves that incorporate and protect a variety of nesting sites that these small local groups depend on for their survival. [ABSTRACT FROM AUTHOR]

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations. [ABSTRACT FROM AUTHOR]

The reproductive biology ofCrax globulosais virtually unknown, this knowledge comprised of only a few anecdotal notes. We found nine nests ofCrax globulosain the middle section of the Juruá River, western Brazilian Amazon, during the dry season. Nests averaged 22.5 m from water and 13.3 m above the ground. We observed two nest types: five made of twigs, leaves and vines, and four within a bromeliad. All nests contained two eggs, but six (67%) were subsequently predated. A female tagged with a transmitter nested twice during the same breeding season. A chick was monitored together with its parents for > 10 months. In addition to hunting and habitat loss, nest predation could be another threat to this endangered species. [ABSTRACT FROM AUTHOR]

Platyrrhine primate taxonomy is a rapidly evolving area of research. The recent description of the Parecis titi monkey, Plecturocebus parecis, has raised substantial questions regarding the taxonomy, distribution, and evolutionary history of titi taxa from south-central Amazonia. There is only a single documented record of P. parecis, which is the type locality, with uncertainty regarding species monophyly. Moreover, there are questions surrounding the distribution and pelage patterns of the poorly studied P. cinerascens and P. parecis, which further highlight the uncertainty regarding the taxonomic validity of this new species. Here, we investigate the taxonomy, distribution, and evolutionary history of these lineages through new field work and assessment of pelage pigmentation patterns from 25 localities, as well as maximum likelihood and Bayesian phylogenetic reconstructions based on two mitochondrial and 11 nuclear loci for 19 and 10 specimens of Plecturocebus, respectively. Our mitochondrial results recover a paraphyletic arrangement for the four P. parecis type specimens that show three distinct haplotypes, with the holotype showing a close affinity to P. bernhardi. Our morphological analysis reveals a north–south clinal bleaching gradient through the Aripuanã-Sucundurí/Juruena interfluve from an all-grayish morphotype associated with P. cinerascens, through intermediary morphotypes with increasingly whitish hairs on the beard, hands, feet, and tail, to the most whitish morphotype described as P. parecis. Based on these findings, we present hypotheses to explain the taxonomy, distribution, and evolutionary history of P. cinerascens and P. parecis and discuss the significance of introgression among titi taxa from southern Amazonia given the lack of study systems for natural hybridization in platyrrhine primates. [ABSTRACT FROM AUTHOR]

We analyzed DNA at 9 microsatellite loci from hair samples of 73 pied tamarins (Saguinus bicolor) located in 3 urban forest fragments and a biological reserve in the city of Manaus, Amazonas, Brazil. The forest fragments had become isolated from the continuous forest 6-15 years prior to the time of sampling. Tests for reduction in population size showed that all groups from the urban forest fragments had undergone genetic bottlenecks. Pied tamarins in this region historically formed one biological population, and the fragments were connected by high levels of gene flow. These results indicate the need to implement a conservation plan that allows for connectivity between the urban fragments, as well as protection from further constriction. Such connectivity could be achieved via the creation and protection of corridors. In addition to the current population trends explained by anthropogenic actions, the species also shows a trend of long-term demographic decline that has resulted in approximately an order of magnitude decrease and began 13 thousand years ago. [ABSTRACT FROM AUTHOR]

We analyzed DNA at 9 microsatellite loci from hair samples of 73 pied tamarins (Saguinus bicolor) located in 3 urban forest fragments and a biological reserve in the city of Manaus, Amazonas, Brazil. The forest fragments had become isolated from the continuous forest 6-15 years prior to the time of sampling. Tests for reduction in population size showed that all groups from the urban forest fragments had undergone genetic bottlenecks. Pied tamarins in this region historically formed one biological population, and the fragments were connected by high levels of gene flow. These results indicate the need to implement a conservation plan that allows for connectivity between the urban fragments, as well as protection from further constriction. Such connectivity could be achieved via the creation and protection of corridors. In addition to the current population trends explained by anthropogenic actions, the species also shows a trend of long-term demographic decline that has resulted in approximately an order of magnitude decrease and began 13 thousand years ago. [ABSTRACT FROM AUTHOR]

Hybridization and introgression have important consequences in evolution, such as increasing the genetic diversity and adaptive potential of a species. One of their most conspicuous footprints is discordance among gene trees or between genes and phenotypes. However, most studies that report introgression fail to disprove the null hypothesis that genetic incongruence may result from stochastic sorting of ancestral allelic polymorphisms. In the case of ancient introgression, these two processes may be especially difficult to distinguish topologically, but they make different predictions about the patterns of coalescence among loci. Here we apply three methods, molecular dating, multispecies coalescent models, and gene tree simulation under coalescence, to compare these two hypotheses that explain the polyphyletic mtDNA of the butterfly peacock bass, Cichla orinocensis. In comparison with a species tree based on 20 unlinked nuclear loci, we determined that mtDNA divergences were too recent to be explained by ancestral polymorphism. Similarly, coalescent species tree branches were significantly shorter when putative introgressed mtDNA was incorporated, and simulations showed the mtDNA topology to be unlikely under lineage sorting only. We conclude that introgression approximately 1.5 million years ago resulted in capture by C. orinocensis of an mtDNA lineage ancestral to the modern subspecies C. oc. monoculus. [ABSTRACT FROM AUTHOR]

Highlights: [•] Twenty-one nuclear loci with a median of 14 variable sites per locus were used to infer a phylogeny of Cichla. [•] There was low resolution, allele sharing, and significant discordance among the observed gene trees. [•] Three different analytical techniques recovered similar phylogenies of delimited species. [•] Loci with few variable sites still contributed important phylogenetic signal. [•] Confidence internals for node ages in the coalescent tree were wide despite many loci. [ABSTRACT FROM AUTHOR]

With the goal of contributing to the taxonomy and systematics of the Neotropical cichlid fishes of the genus Symphysodon, we analyzed 336 individuals from 24 localities throughout the entire distributional range of the genus. We analyzed variation at 13 nuclear microsatellite markers, and subjected the data to Bayesian analysis of genetic structure. The results indicate that Symphysodon is composed of four genetic groups: group PURPLE—phenotype Heckel and abacaxi; group GREEN—phenotype green; group RED—phenotype blue and brown; and group PINK—populations of Xingú and Cametá. Although the phenotypes blue and brown are predominantly biological group RED, they also have substantial contributions from other biological groups, and the patterns of admixture of the two phenotypes are different. The two phenotypes are further characterized by distinct and divergent mtDNA haplotype groups, and show differences in mean habitat use measured as pH and conductivity. Differences in mean habitat use is also observed between most other biological groups. We therefore conclude that Symphysodon comprises five evolutionary significant units: Symphysodon discus (Heckel and abacaxi phenotypes), S. aequifasciatus (brown phenotype), S. tarzoo (green phenotype), Symphysodon sp. 1 (blue phenotype) and Symphysodon sp. 2 (Xingú group). [ABSTRACT FROM AUTHOR]

Abstract: We investigated demographic history and population structuring of Colossoma macropomum sampled from 14 localities in the Amazon basin and the Bolivian sub-basin; the two basins are separated by a series of 16 rapids. Although genetically differentiated, IMa analyses suggest non-zero bi-directional migration rates, and inter-basin divergence of approximately 17 thousand years ago. Analyses in BEAST indicated that Bolivian C. macropomum has been demographically stable except for a moderate population increase in the last 12 thousand years, while Amazonian C. macropomum has been experiencing demographic growth over the last 350 thousand years, resulting in approximately one order of magnitude increase in coalescent Ne . [Copyright &y& Elsevier]

Abstract: We carried out a phylogeograhic and population genetic analysis of fishes of the taxonomically contentious genus Symphysodon from the Amazon basin in order to test hypotheses of relationships among taxonomic units, and potential processes driving diversification within this genus. We sampled 334 individuals of the genus Symphysodon from 24 localities that span the complete geographic distribution of this genus. The sampling scheme included all known phenotypic groups, species and subspecies. Analyses were based on 474bp of the mitochondrial control region and 1443bp of the exon 3 of RAG1 gene. We observed 102 mtDNA haplotypes defined by 89 segregating sites, and 5 nuDNA alleles defined by three segregating sites. Maximum-likelihood, Bayesian-inference and statistical parsimony analyses revealed three well defined monophyletic groups. These clades corresponded to the ‘green’ and ‘blue’ groups of Symphysodon aequifasciatus, and to a previously morphologically unrecognized clade from the Xingu River drainage. These three clades were nested within a paraphyletic assemblage consisting of the ‘brown’ group of S. aequifasciatus and of both described subspecies of S. discus, the ‘Heckel’ and the ‘abacaxi’ discus. Nuclear allele sharing was observed among groups, but there were significant differences in frequencies. We inferred several processes including past fragmentation among groups, and restricted gene flow with isolation by distance within the paraphyletic ‘brown+Heckel+abacaxi’ groups, and suggest that differences among the ‘blue’, ‘Heckel’ and ‘brown’ groups are potentially maintained by differences in water chemistry preferences. We further inferred colonization of the western Amazon basin by an ancestor of the ‘green’ clade. The ‘green’ group was the only group with a pattern of haplotype distribution consistent of a demographic expansion, and the divergence of this clade from other groups of discus was consistent with recent geologic evidence on the breach of the Purus Arch which separates western Amazon from eastern Amazon. We further hypothesized that the differentiation of the ‘Xingu’ clade could be due to vicariance events resulting from Pleistocene sea level, and thus Amazon River level fluctuations. We discuss the bearings of our results on the current taxonomy of this group, and on the biological reality of the different forms, subspecies and species of Symphysodon concluding that we are probably observing a process of diversification, and therefore taxonomy will remain contentious. [Copyright &y& Elsevier]

A fragment of 600 bp of the gene which codes for the surface antigen of hepatitis B virus (HBV) was amplified and sequenced from patients who were born in five states of the Brazilian Amazon (Amazonas, Pará, Acre, Rondônia and Tocantins). A total of 44 sequences were used for the estimation of molecular genetic parameters and phylogenetic analyses. Compared with patients who were asymptomatic, those who had acute hepatitis and chronic liver disease had higher levels of genetic variability and higher rates of nucleotide substitutions. The analysis of transition and transversion substitutions showed that transition-type substitutions predominated. In chronic liver disease carriers, transversion-type substitutions showed phylogenetic saturation. In general, all of the analyses carried out in this study showed an association between patterns of changes in molecular genetic parameters and the stage of disease progression. Phylogenetic analysis using the HKY85 model of evolution identified 41 individuals as genotype A, suggesting its predominance in the Amazon region, one individual as genotype C, and one individual closely related to genotypes E and F. [ABSTRACT FROM AUTHOR]

We conducted a population genetic analysis of the two Amazonian tortoises, Chelonoidis denticulata (n = 40) and Chelonoidis carbonaria (n = 39) in a region of sympatry within the Xingú River basin. High levels of gene flow among sampled localities indicated lack of population structure for both species. Genetic parameters indicated a moderate level of genetic diversity in C. denticulata and neutrality tests suggested that populations of this species were in demographic equilibrium with respect to mitochondrial DNA. On the other hand, C. carbonaria presented low levels of genetic diversity and a signal of population expansion. Most records of C. denticulata are from areas of humid forest while those for C. carbonaria are from areas of semi-deciduous forests and transitional areas between humid and semi-deciduous forests. Therefore, the demographic expansion observed in C. carbonaria population could reflect an increase in the availability of suitable habitats for this species due to anthropogenic or natural processes. Additionally, we observed haplotype sharing between these two tortoise species indicating hybridization or incomplete lineage sorting. [ABSTRACT FROM AUTHOR]

The northern mangrove coast of Brazil comprises the Brazilian states of Amapá, Pará and Maranhão. Fishes from the coastal mangrove region form a principal component of the local fishery, and account for 58% of all fish landed. The most commonly landed fishes are those of the family Sciaenidae. Cynoscion acoupa is one of the most exploited sciaenid species, with over 600 tons landed each year. Therefore, we developed 17 microsatellite markers to investigate genetic variability and population structuring of this species along the coast of Brazil. [ABSTRACT FROM AUTHOR]

The present study reports the first population genetic analysis of Arapaima gigas, an important but critically over-exploited fish species of the Amazon basin. We sequenced two discontinuous mitochondrial DNA regions of 1204 base-pairs (bp) (NADH1 segment) and 1143 bp (ATPase segment) from 139 individuals of A. gigas representing eight localities spanning the Amazon basin from Iquitos, Peru to Macapá, Brazil. We discovered 34 haplotypes separated by 44 segregating sites. The two most common haplotypes are shared among all populations and isolation-by-distance appears to be the most important population dynamic, although there is no significant association between geographical distance and genetic differentiation. Observed patterns of differentiation appear to be attributable largely to anthropogenic factors associated with over-exploitation. Greatest haplotypic diversity exists upstream of Manaus and in areas away from large centres of population. The female variance and inbreeding effective population sizes are approximately 150 000 individuals and localities in the Amazon basin are connected by gene flow. Naturally low levels of population differentiation and relatively high between-population connectivity is encouraging for the conservation and management of A. gigas. If strategically placed biological reserves were created throughout the Amazon basin to act as sources of emigrants within a source--sink metapopulation model, we believe locally depleted populations can be re-populated and maintained by individuals immigrating from these reserves. [ABSTRACT FROM AUTHOR]

The accumulation of studies delimiting species in Amazonia has not only shed light on the patterns of its outstanding species richness but also allowed a better understanding of the processes of diversification within this immense region. Nevertheless, vast knowledge gaps remain even for prominent anuran species complexes, such as the Rhinella margaritifera species group. This clade of toads comprises 23 valid species-level taxa, mainly distributed in Amazonia but also in South America's Dry Diagonal and Atlantic and trans-Andean rainforests. Species boundaries and taxonomy in this group are notoriously complex, with studies suggesting the existence of several unnamed species. Available phylogenetic information suggests an Andean-western Amazonian origin of the group with subsequent diversification within Amazonian lowlands during the last 10 Myr and secondary dispersals into other Neotropical regions. To further test this biogeographic scenario and improve knowledge on species diversity, we used an unprecedentedly large mtDNA sampling (>800 16S sequences) across the clade's distribution and comprising all but one described species. We delimited 54 Molecular Operational Taxonomic Units, which we tested further based on patterns of variation of a nuclear locus and acoustic and morphological data. This approach confirmed the existence of at least 25 candidate species, 19 of which correspond to currently recognized taxa whereas 30 remained 'unconfirmed'. Our results clarify the taxonomic status of some species but also suggest multiple introgression events that blur some mtDNA-based species boundaries. Lastly, to provide a temporal framework for the clade's diversification, we generated a time-calibrated phylogenetic tree based on a mitogenomic matrix, which confirmed a Miocene (∼9 Ma) western Amazonian origin and six major clades in the group, each having initially diversified in different regions within Amazonia. Most of these clades have later dispersed throughout Amazonia during the establishment of the modern Amazonian hydrographic system, i.e., in the last 6 Myr. [ABSTRACT FROM AUTHOR]

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics. Population study of whole genomes of wild uakary monkeys (Cacajao genus) exposes how the dynamic and highly heterogeneous Amazon basin may have shaped complex connectivity patterns and driven fast population differentiation on these. [ABSTRACT FROM AUTHOR]

Morphology has been used to establish interspecific limits in echimyid rodents. However, using only morphology can be problematic, especially for polymorphic or morphologically cryptic species. Recently, combined data sources have been used to recognize and delimit species and have proven to be especially useful for taxonomic resolutions. Makalata is a taxonomically problematic genus that needs revision. Currently, two species are recognized: M. didelphoides and M. macrura. A third species, M. obscura, is considered questionable. Molecular studies demonstrate that diversity in the genus has been underestimated. In the present study, we identified 14 subclades representing potential species in the genus Makalata using molecular and cytogenetic data. Analysis of species delimitation corroborated this hypothesis. Four lineages in the Guiana Shield, currently considered to be a single taxonomic entity in the literature (M. didelphoides) based only on morphology, were shown to be potential cryptic species, differentiated only by molecular and karyotype data. We verified that the name M. didelphoides cannot be applied to any clade or museum specimen without a genetic approach and sequencing of the holotype. We present an amended diagnosis for M. macrura through examination of the original description, sequencing, and karyotype of topotypic samples allowed us to associate with the name M. macrura represented by subclade I in this study. Karyotype data proved to be a powerful tool in differentiating the Makalata species according to different combinations of diploid number (2n) and fundamental number, as for other genera of spiny tree‐rats. Our results demonstrate a heterogeneous status for Makalata, highlighting the importance of using multiple tools to determine the taxonomy of this group and reinforcing the importance of molecular and chromosomal data added to the morphological data to obtain a more accurate picture of the taxonomic diversity of this and other small mammal genera. [ABSTRACT FROM AUTHOR]

Aim: The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota. Here, we tested how river rearrangements influenced the evolutionary history of uakari monkeys, genus Cacajao, a primate genus primarily associated with seasonally flooded forests in central and western Amazonia. Location: Central and Western Amazonia. Taxon: The genus Cacajao, including the black uakaris (C. melanocephalus, C. ayresi, C. hosomi); and the bald‐headed uakaris (C. calvus, C. amuna, C. rubicundus, C. ucayalii, C. novaesi). Methods: We performed a continuous phylogeographic analysis using 77 cytochrome b sequences to identify the origin and dispersal of Cacajao lineages. We used genome‐wide SNP variation (ddRADseq) to investigate population structure, gene flow and demographic history in Cacajao populations and used digital elevation models to identify landscape and riverscape characteristics that may have influenced the geographic distribution of Cacajao. Results: Our continuous phylogeographic reconstruction pointed out that the ancestral Cacajao lineage occupied the flooded forests of the Solimões River, in central Amazonia, at ~1.7 Mya and descendant lineages dispersed throughout central and western Amazonia more recently. We identified gene flow in both black and bald‐headed uakari populations, even across rivers considered barriers (e.g. the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. Historical demographic analyses suggest varied scenarios of population size changes among Cacajao monkeys consistent with periods of intense dynamism in flooded habitats and the formation of non‐flooded upland forests. Main Conclusion: Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent changes in demographic histories in species with a restricted geographic distribution. [ABSTRACT FROM AUTHOR]

Presently, Myloplus schomburgkii is the most easily recognized species among the serrasalmids by having a vertical black bar in the middle of the body. However, through a broad taxonomic review, including DNA barcoding and morphological analyses, we were able to identify and describe two new species that also share a dark vertical bar on the flank. In addition, we redescribe M. schomburgkii, designating a neotype and restricting the type-locality to rio Negro in Barcelos, Amazonas State, Brazil. The three lineages of black-barred pacus present high molecular divergences (7.9-11%) and can be distinguished by differences in the shape of the vertical bar, shape of females' anal fin, number of total vertebrae, number of total branched dorsal-fin rays, among other characters. Although the existence of these two new species has been hidden due to many morphological similarities, mainly the presence of the black bar, the three lineages do not compose a monophyletic group, with one of the new species being recovered as sister to Ossubtus xinguense. This result reinforces the necessity of the redefinition of the Myleini genera. [ABSTRACT FROM AUTHOR]

An abstract of the article "Detection of polyandric behavior in giant Amazonian river turtle (Podocnemis expansa) using microsatellites markers" by Juliana Morais, Izeni Farias and colleagues is presented.

​​​​​​​The so-called arc of deforestation is a major agricultural and industrial frontier in southern Amazonia and northern Cerrado of Brazil. As arboreal mammals, the primates in this region are therefore threatened by forest loss and fragmentation. At the same time, knowledge about the taxonomic diversity and distribution ranges of these taxa is incomplete, which might hamper efficient conservation measurements. New species have been recently discovered in this region, and their ranges remain imprecise because only a few occurrence records are available for each species. Here we present 192 new records of 22 species and subspecies of Alouatta, Aotus, Ateles, Cebus, Chiropotes, Lagothrix, Leontocebus, Pithecia, Plecturocebus, Saimiri, and Sapajus, collected in 56 different localities during 10 field expeditions across the arc of deforestation between 2015 and 2018. Based on these new records, we extend the ranges of Alouatta puruensis, Ateles chamek, and Saimiri collinsi; identify potential hybridization zones between A. puruensis and A. discolor, and between At. chamek and At. marginatus; redefine the range of Plecturocebus moloch; and clarify the ranges of P. baptista and P. hoffmannsi. Moreover, these results and the dataset are valuable for further research on, for example, species distribution and habitat use modeling, for assessing species extinction risks, and for supporting efforts for the conservation of species increasingly threatened on a global deforestation frontier. [ABSTRACT FROM AUTHOR]

The incidence of multiple paternities in two populations of Podocnemis expansa of Brazilian Amazon both rose in captivity and in natural habitat, was verified by using five microsatellite loci. Three hundred twenty-seven offspring from two different sampling sites were genotyped. The analysis revealed a 100% rate of multiple paternities in both populations. The Mendelian distribution of the alleles found in each nest was used to determine the number of contributing males. It was estimated that at least ten males contributed to each brood in captivity and nine contributed to each brood in the wild. These values are the highest ever recorded for the number of contributing P. expansa males. The findings have considerable implications regarding the conservation of this species, given that multiple paternities is important to the maintenance of genetic variability and has important consequences in increasing the effective size of a population in comparison to single paternities. [ABSTRACT FROM AUTHOR]

The genus Saguinus comprises three principal clades that diverged in the Middle to Late Miocene. Their taxa are ecologically differentiated and allopatrically distributed. These clades were recently recognized as different genera, Saguinus, Tamarinus and Oedipomidas. In Tamarinus, the phylogenetic relationships among species/subspecies are poorly understood. Thus, in this study we present a comprehensive dated genomic phylogeny based on double digest restriction associated DNA for all known species and subspecies of Tamarinus. We also tested whether that Tamarinus imperator and Tamarinus subgrisescens are different species, as morphology‐based taxonomy, phenotypical divergences and mitochondrial genes recognized them as two different species. Additionally, we reconstructed time‐calibrated phylogenetics tree hypotheses of all extant species and subspecies of the genera Saguinus, Tamarinus and Oedipomidas. Our analysis robustly supported the phylogenetic hypothesis of all species/subspecies of the genus Tamarinus; strongly supported a divergence between the three clades, Saguinus, Oedipomidas and Tamarinus; and provided support for T. imperator and T. subgrisescens as distinct species. Therefore, we reiterate and ratify the division of Saguinus into three genera, supporting the taxonomic proposal for these genera. [ABSTRACT FROM AUTHOR]

Platyrrhinus guianensis is bat with a distribution restricted to the Guiana Region of South America in Guyana and Suriname. Herein, we report the southernmost record of this species, extending its distribution to Brazil in Brazilian Amazon. Our record indicates that the species have a larger geographical range that previously thought. Platyrrhinus guianensis occurs in sympatry with Platyrrhinus brachycephalus, Platyrrhinus incarum, and Platyrrhinus fusciventris in the Brazilian Amazon, and can be confused with these species, raising the possibility that there might be other specimens of Platyrrhinus guianensis misidentified as other species in scientific collections. [ABSTRACT FROM AUTHOR]

The discovery and characterization of cryptic diversity is important for conservation and management, especially for ichthyofauna, whose diversity is underestimated and understudied. Cryptic diversity is especially common in widely distributed species, and Pellona flavipinnis is one such species. Thus, the aim of the present study was to investigate and test whether P. flavipinnis harbours cryptic diversity. In this study we used the COI and control region sequences and microsatellite loci of 86–114 specimens from 11–12 locations throughout the Amazon basin, depending on the molecular marker used. We also included two COI GenBank sequences from the type locality of the species, the Paraná River. The results from COI sequences showed that P. flavipinnis from the Amazon basin presented two spatially structured lineages differentiated from P. flavipinnis from the Paraná River by 10.6%–9.8% (depending on the lineages) and 45 mutational steps. The genetic distance between the Amazon lineages was 2.4% using COI, with high population differentiation values (ФST = 0.8686 and ФST = 0.8483 for COI and control region, respectively). Among the five species delimitation methods employed, three indicated two lineages in P. flavipinnis in the Amazon basin, and all five methods indicated that the Amazonian lineages are different from that of Paraná. Results from microsatellite loci also showed that P. flavipinnis from the Amazon basin is composed of two evolutionary units. The results of 13 morphometric measurements indicated that there are no differences in shape between the P. flavipinnis lineages in the Amazon basin. The present findings suggest that there are two sympatric lineages of P. flavipinnis in the Amazon basin. [ABSTRACT FROM AUTHOR]

Currently, 15 species of Amazon marmosets (genus Mico) are known to science. The Amazon marmosets occur primarily in southern Brazilian Amazonia, the arc of deforestation, and are among the least studied primates of the neotropics. This is particularly the case for M. acariensis and M. chrysoleucos, both endemic to the Aripuanã–Sucundurí interfluve, south-central Amazonia. Mico acariensis was not studied beyond the species description, and the only information currently available is the pelage colouration of the holotype, inferred coordinates of the type locality, and a field report with two additional localities of occurrence. Regarding M. chrysoleucos, in addition to the species description, there are taxonomic reviews, the report of a second occurrence record, and a study on the species range. We provide here new occurrence records that extend the distribution of M. chrysoleucos; provide new records for and update the distribution of M. acariensis; and propose the existence of a hybrid zone in the Aripuanã–Sucundurí interfluve, i.e. around the known distribution boundaries of M. acariensis, M. chrysoleucos, and M. melanurus, and we also discuss habitat use patterns of Amazon marmosets. [ABSTRACT FROM AUTHOR]

Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes. [ABSTRACT FROM AUTHOR]

The brown or pouchless four-eyed opossums or jupatis represent the genus Metachirus with a wide geographical range in the Neotropics. Recent studies show distinct monophyletic clades with high genetic divergence and recognized two species, Metachirus nudicaudatus and Metachirus myosuros. Nevertheless, there is a need for systematic revision with multiple sources of evidence on the taxonomy of Metachirus, which has never been fully revised. Here we describe a new species of Metachirus for the Brazilian Amazon from the Xingu/Tocantins interfluve using the unification of concepts and evolutionary significant units, morphological, genetic, and geographic data. Our analysis reveals a new species within Metachirus as a differentiated Amazonian clade from the Serra dos Carajás region and the Caxiuanã National Forest, both in the Xingu endemism centre. This new species can be distinguished from the type species, M. nudicaudatus and from M. myosuros through discrete external morphological characters, including cranium and dentition, and molecular data with an average degree of divergence, but ancient divergence time for the mitochondrial cytochrome b gene. The Amazon River delimits the distribution of the new species, which also occurs in areas under strong anthropogenic pressure, reinforcing the importance to guide conservation strategies for the region. [ABSTRACT FROM AUTHOR]

The freshwater fish Piaractus brachypomus is an economically important for human consumption both in commercial fisheries and aquaculture in all South American countries where it occurs. In recent years the species has decreased in abundance due to heavy fishing pressure. The species occurs in the Amazon and Orinoco basins, but lack of meristic differences between fishes from the 2 basins, and extensive migration associated with reproduction, have resulted in P. brachypomus being considered a single panmictic species. Analysis of 7 nuclear microsatellites, mitochondrial DNA sequences (D-loop and COI), and body shape variables demonstrated that each river basin is populated by a distinct evolutionarily significant unit (ESU); the 2 groups had an average COI divergence of 3.5% and differed in body depth and relative head length. Historical connection between the 2 basins most probably occurred via the Rupununi portal rather than via the Casiquiare canal. The 2 ESUs will require independent fishery management, and translocation of fisheries stocks between basins should be avoided to prevent loss of local adaptations or extinction associated with outbreeding depression. Introductions of fishes from the Orinoco basin into the Putumayo River basin, an Amazon basin drainage, and evidence of hybridization between the 2 ESUs have already been detected. [ABSTRACT FROM AUTHOR]

The freshwater fish Piaractus brachypomus is an economically important for human consumption both in commercial fisheries and aquaculture in all South American countries where it occurs. In recent years the species has decreased in abundance due to heavy fishing pressure. The species occurs in the Amazon and Orinoco basins, but lack of meristic differences between fishes from the 2 basins, and extensive migration associated with reproduction, have resulted in P. brachypomus being considered a single panmictic species. Analysis of 7 nuclear microsatellites, mitochondrial DNA sequences (D-loop and COI), and body shape variables demonstrated that each river basin is populated by a distinct evolutionarily significant unit (ESU); the 2 groups had an average COI divergence of 3.5% and differed in body depth and relative head length. Historical connection between the 2 basins most probably occurred via the Rupununi portal rather than via the Casiquiare canal. The 2 ESUs will require independent fishery management, and translocation of fisheries stocks between basins should be avoided to prevent loss of local adaptations or extinction associated with outbreeding depression. Introductions of fishes from the Orinoco basin into the Putumayo River basin, an Amazon basin drainage, and evidence of hybridization between the 2 ESUs have already been detected. [ABSTRACT FROM AUTHOR]

Colour variation in crocodilians is associated with size, environment and genetic structure, but little is known about colour variation in the genus Paleosuchus (Alligatoridae). Different genetic lineages of Paleosuchus palpebrosus (Dwarf caiman) occupy different environments throughout the species extensive distribution, and all are cryptically coloured. We captured 187 P. palpebrosus and recorded their head colour from four genetically distinct geographic clades between 2008 and 2019. Additionally, we determined the jaw and belly spot pattern of a subsample of 95 individuals (22–109 cm snout-vent length). PERMANCOVA was used to investigate the relationships between head colour and spot patterns, to the caiman size, sex, and geographic lineage, as well as ambient temperature. Variation in head colour, and jaw and belly spot patterns, were related to genetic lineage, snout-vent length and temperature, but the model explained only ∼45.4% of the variance in the data. Sex was not significantly related to the head colour, or jaw and belly spot patterns. Dwarf caimans inhabiting cooler climates tend to be darker than individuals from warmer areas, and individuals from the "Cerrado-Pantanal" and "Bolivia" lineages generally darker than the "Amazon" and "Madeira" lineages. However, individuals of a given size in different lineages overlap greatly in colour patterns and colour alone could not be used to distinguish lineages. The Natterer's hypothesis of head-colour as diagnose from "Cerrado-Pantanal" lineage, cannot be completely accepted according our quantitative analysis, although there are a variation in the geographic distribution of these phenotypic traits, and the "Cerrado-Pantanal" lineage had been the most distinct among the lineages. [ABSTRACT FROM AUTHOR]

The spread of non-native fish species is increasing globally and threatening aquatic ecosystems. Identifying the origins, the pathways, and vectors is crucial for managing biological invasions. We conducted a genetic characterization of Arapaima gigas from the Madeira River, considering native and non-native populations, to elucidate the invasion of the upper and middle Madeira River basin by A. gigas. We analyzed 9 microsatellite loci of 141 individuals from native (lower Madeira) and invasive (upper Madeira) populations, in addition to a locality from Peru outside the Madeira River basin drainage area, that previously was suggested to be one of the possible origins of the invasion. The results of discriminant analysis of principal components, Bayesian modeling of population structure, clustering and assignment tests (using microsatellite data from other Amazon locations) showed a clear separation between native and invasive populations and revealed a mixture of individuals from upper and middle Madeira and Peru. We confirm that the invasive population originates from Peru and was introduced by fish escapees from farms. Multiple secondary introductions may have advanced the invasion speed. Such a scenario represents a conservation paradox, because in its native habitat, A. gigas is endangered, whereas it has become invasive in non-native areas. [ABSTRACT FROM AUTHOR]

Based on morphological and molecular analysis of Astronotus species, a new species is described from the Orinoco River and Gulf of Paria basins in Venezuela and Colombia. Morphologically, it differs from Astronotus crassipinnis and Astronotus ocellatus in pre-orbital depth, caudal peduncle depth, head width, and caudal peduncle length, with significant differences in average percentage values. Osteologically, it differs from the two described species by lacking a hypurapophysis on the parahypural bone (hypural complex) and having two or three supraneural bones. Another characteristic that helps diagnose the new species is the morphology of the sagitta otolith, which is oval with crenulated dorsal and ventral margins and a rounded posterior edge. Genetically, the new species is distinct from all the other lineages previously proposed for the genus, delimited by five single locus species delimitation methods, and also has unique diagnostic nucleotides. Phylogenetic analyses support the monophyly of the new species as well as all other species/lineages. Astronotus species have considerable genetic, anatomical, and sagitta otolith shape differences, but have few significant traditional morphometric and meristic differences, because there is high variability in counts of spines, soft dorsal-fin rays, and lateral-line scales. It is clear that this new species is genetically and anatomically differentiated from all other species within the genus, and deserves recognition as a new valid species. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines. [ABSTRACT FROM AUTHOR]

The untufted, or gracile, capuchin monkeys are currently classified in four species, Cebus albifrons, C. capucinus, C. olivaceus, and C. kaapori, with all but C. kaapori having numerous described subspecies. The taxonomy is controversial and their geographic distributions are poorly known. Cebus albifrons is unusual in its disjunct distribution, with a western and central Amazonian range, a separate range in the northern Andes in Colombia, and isolated populations in Trinidad and west of the Andes in Ecuador and northern Peru. Here we examine previous morphological and molecular hypotheses of the taxonomy and phylogeny of Cebus. We construct a time-calibrated phylogeny based upon mitochondrial DNA sequences from 50 Cebus samples from across their range. Our data indicate that untufted capuchins underwent a radiation at about 2 Ma, and quickly diversified in both the Andes and the Amazon. We provide a provisional reassessment for the taxonomy of untufted capuchins in the Amazon, the Llanos, the Andes, Trinidad, and Central America, splitting currently paraphyletic taxa into several species, including: at least two Amazonian species ( C. yuracus and C. unicolor); a species from the Guiana Shield (most likely the same as Humboldt's C. albifrons); two northern Andean species, C. versicolor, C. cesarae; C. brunneus (with trinitatis a junior synonym) on the Venezuelan coast, and C. adustus in the region of Lake Maracaibo; C. capucinus in northwestern Ecuador and Colombia, and Panama; C. imitator in Central America; C. olivaceus and C. castaneus occupying a large part of the Guiana Shield; and C. kaapori in the eastern Amazon, south of the Rio Amazonas. More intensive and extensive geographic sampling is needed, including that for some subspecies not represented here. Taxa from the southwestern Amazon ( yuracus, cuscinus, and unicolor) and the phylogenetic position of Humboldt's Simia albifrons from the Orinoco remain particularly poorly defined. Am. J. Primatol. 74:381-393, 2012. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Background: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). Results: We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. Conclusions: Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity. [ABSTRACT FROM AUTHOR]

We attempted to distinguish spring passage migrant Tropical Kingbirds (Tyrannus melancholicus) from resident conspecifics where they overlap in South America. Migrant males at our Bolivian study site had significantly less tail feather molt and longer wing chords than resident males. Migrant females had significantly longer wing chords, less flight feather molt, and less flight leather wear than resident females. We found no evidence of genetic population differentiation between migrants and residents. We also compared wing chords of migrants and residents to those of breeding kingbirds in breeding populations further south. Wing chords of migrants were more similar to those of breeders from further south than to those of breeders at our study site. An ability to distinguish migrant from resident conspecifics will be critical to understanding migrant winter ecology, migratory routes, and connectivity of migratory populations in South America. [ABSTRACT FROM AUTHOR]

Osteoglossum bicirrhosum (silver arowana) is an important fish for the economy of the Amazon region, both as an ornamental fish and as a food fish. To provide tools for addressing ecological and genetic questions, we developed 19 polymorphic microsatellite markers that had between 2 and 7 alleles per locus in the 24 tested individuals. The transferability of many of the loci was confirmed for Osteoglossum ferreirai (black arowana) and Arapaima gigas, and for three African osteoglossiform species. [ABSTRACT FROM AUTHOR]

Abstract: Microsatellite DNA polymorphisms were screened in seven populations of the largest Neotropical predator, the Black caiman Melanosuchus niger (n =169), originating from Brazil, French Guiana and Ecuador. Eight loci were used, for a total of 62 alleles. The Ecuadorian population had the lowest number of alleles, heterozygosity and gene diversity; populations of the Guianas region exhibited intermediate diversities; highest values were recorded in the two populations of the Amazon and Rio Negro. During the last century Melanosuchus populations have been reduced to 1–10% of their initial levels because of hunting pressure, but no strong loss of genetic diversity was observed. Both the inter-locus g-test and the Pk distribution suggested no recent important recovery and/or expansion of current populations. On a global scale, the inter-population variation of alleles indicated strong differentiation (F ST =0.137). Populations were significantly isolated from each other, with rather limited gene flow; however, these gene flow levels are sufficiently high for recolonization processes to effectively act at regional scales. In French Guiana, genetic structuring is observed between populations of two geographically close but ecologically distinct habitats, an estuary and a swamp. Similar divergence is observed in Brazil between geographically proximate “black water” and “white water” populations. As a consequence, the conservation strategy of the Black caiman should include adequate ecosystem management, with strong attention to preservation of habitat integrity. Distribution of genetic diversity suggests that current populations originated from the central Amazonian region. Dispersal of the species may thus have been deeply influenced by major climatic changes during the Holocene/Pleistocene period, when the Amazonian hydrographic networks were altered. Major ecological changes such as glaciations, marine transgressions and a hypothesized presence of an Amazonian Lake could have resulted in extension of Black caiman habitats followed by isolation. [Copyright &y& Elsevier]

Phylogeographic patterns in Macrodon ancylodon sampled from 12 locations across all its range were investigated using mitochondrial DNA cytochrome b sequences, and analysed together with patterns of morphometric differentiation. Populations of the North Brazil and the Brazil currents, with warmer waters, form a clade (tropical clade) separated by 23 fixed mutations from the populations that inhabit regions of colder waters influenced by the Brazil and Malvinas currents (subtropical clade). No gene flow exists between the tropical and subtropical clades, and most likely also between the two groups of the tropical clade. Distribution of these clades and groups is correlated with flow of currents and their temperatures, and is facilitated by larval retention and low adult migration. Despite differentiation at the molecular level, fishes analysed from all these current-influenced regions are morphometrically homogeneous. Throughout its range M. ancylodon inhabits the same, or very similar niche; thus, stabilizing selection probably promotes the retention of highly conserved morphology despite deep genetic divergence at the mitochondrial DNA cytochrome b. [ABSTRACT FROM AUTHOR]

We used mitochondrial DNA control region sequences to examine phylogeography and population differentiation of the endangered Amazonian manateeTrichechus inunguis. We observe lack of molecular differentiation among localities and we find weak association between geographical and genetic distances. However, nested clade analysis supports restricted gene flow and/or dispersal with some long-distance dispersal. Although this species has a history of extensive hunting, genetic diversity and effective population sizes are relatively high when compared to the West Indian manateeTrichechus manatus. Patterns of mtDNA haplotype diversity inT. inunguissuggest a genetic disequilibrium most likely explained by demographic expansion resulting from secession of hunting and enforcement of conservation and protective measures. Phylogenetic analysis ofT. manatusandT. inunguishaplotypes suggests thatT. inunguisis nested withinT. manatus, effectively makingT. manatusa paraphyletic entity. Paraphyly ofT. manatusand recent divergence times ofT. inunguisand the three mainT. manatuslineages suggest a possible need for a taxonomic re-evaluation of the western AtlanticTrichechus. [ABSTRACT FROM AUTHOR]

Turtles are one of the most threatened groups of vertebrates, with about 60% of species classified at some level of extinction risk. Compounding this extinction crisis are cryptic species and species complexes that are evaluated under a single species epithet but harbor multiple species, each of which needs to be evaluated independently. The Phrynops geoffroanus species group is a classic example. Described first in 1812, it is currently thought to harbor multiple species. To test this hypothesis, we collected mitochondrial and nuclear genomic data, morphometric data, and distribution and associated biome information. We applied statistically rigorous species delimitation analyses, taxonomic hypotheses tests, and fully coalescent phylogenetic reconstruction methods, concluding that the Phrynops geoffroanus species complex comprises four geographically structured species/lineages that diverged during the Pleistocene and are currently geographically structured along the main South American river basins and biomes. These species/lineages show subtle and largely non-significant differences in shape but are characterized by differences in coloration and patterns of marks on the head and plastron. Our results contribute to the understanding of species diversity and diversification of biodiversity in South America and provide an important basis for the conservation of freshwater turtles. [ABSTRACT FROM AUTHOR]

A new killifish species, Rivulus duckensis, is described from the Reserva Adolpho Ducke, Manaus, Amazonas, Brazil. It is distinguished from other central Amazonian Rivulus species by maximum body size, adult color pattern, habitat preference and mitochondrial DNA sequences. Based on the phylogenetic analysis of molecular sequence data, our best hypothesis suggests that R. duckensis sister taxon to a clade of Rivulus species occurring in the upper Rio Orinoco basin, Amazonas state, Venezuela and Rivulus rectocaudatus, Amazonas department, Peru. [ABSTRACT FROM AUTHOR]

The state of Florida has the world's highest diversity of established nonnative reptiles, including snakes, lizards, turtles, and crocodilians, most of them introduced from the pet trade. The Spectacled Caiman (Caiman crocodilus) is the only nonnative crocodilian established in Florida, with the earliest date of introduction in 1950. Despite its likely origin being Colombia, the taxonomic identity of the subspecies occurring in Florida remains unknown. We report the first study that resolves the taxonomic status of the population of Ca. crocodilus in Florida based on molecular analysis of samples collected from the 1970s to 2013. We also investigate the probable origin of this population as well as the specimens of the Dwarf Caimans, Paleosuchus palpebrosus and Paleosuchus trigonatus, which have been collected in Florida. We identified only one lineage of Ca. crocodilus in Florida, corresponding to Caiman crocodilus fuscus, and our results indicate the Magdalena River basin in Colombia as the most likely area of origin. We also correct the identification of Paleosuchus recorded in Florida and identify the Guiana Shield, and specifically Guyana, as the most likely region from which these specimens were introduced. [ABSTRACT FROM AUTHOR]

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena–Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation. [ABSTRACT FROM AUTHOR]